Contacts of the helix formed by residues 589 - 597 (chain A) in PDB entry 1TAQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A THR* 1.3 88.4 - - - +
590A LEU* 1.3 57.5 + - - +
592A GLN* 4.0 3.8 - - + +
593A ARG* 2.9 49.1 + - - +
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Residues in contact with LEU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 4.9 0.2 - - + -
463A VAL* 4.1 10.3 - - + -
466A GLU* 4.9 1.8 - - - +
538A LEU* 3.8 32.5 - - + -
541A LEU* 3.6 27.1 - - + -
546A ILE* 4.1 26.5 - - + -
588A THR* 3.2 4.8 + - - +
589A PRO* 1.3 77.9 - - - +
591A GLY* 1.3 59.4 + - - +
592A GLN 3.2 1.8 - - - -
593A ARG* 3.0 33.4 + - + +
594A ILE* 2.8 42.2 + - + +
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Residues in contact with GLY 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A ILE* 4.1 7.0 - - - +
585A PRO* 2.9 39.4 - - - +
588A THR* 2.9 14.3 + - - -
590A LEU* 1.3 71.5 - - - +
592A GLN* 1.3 61.7 + - - +
594A ILE* 3.1 4.9 + - - +
595A ARG* 3.0 31.1 + - - +
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Residues in contact with GLN 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A PRO 4.6 0.2 - - - +
586A VAL* 4.8 0.2 - - - -
587A ARG* 3.2 35.6 + - - +
588A THR 3.1 15.9 + - - +
589A PRO* 4.0 4.5 - - + +
591A GLY* 1.3 75.3 - - - +
593A ARG* 1.3 62.3 + - + +
595A ARG* 3.4 12.4 + - - +
596A ARG 3.4 10.9 + - - -
828A LEU* 3.2 49.0 - - + +
831A LYS* 3.5 34.1 - - + +
832A GLU* 3.8 8.3 + - - +
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Residues in contact with ARG 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 2.8 34.5 + - - +
459A LEU* 4.1 11.4 - - + -
462A GLU* 3.1 24.5 + - - -
463A VAL* 4.9 0.2 - - - +
466A GLU* 2.8 37.2 + - - -
589A PRO* 2.9 34.3 + - - +
590A LEU* 3.0 46.6 + - + +
592A GLN* 1.3 79.8 - - + +
594A ILE* 1.3 61.3 + - - +
596A ARG* 3.3 13.2 - - - +
828A LEU* 5.1 1.3 - - - -
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Residues in contact with ILE 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LEU* 5.9 2.8 - - + +
459A LEU* 4.5 6.5 - - + -
541A LEU* 4.3 15.5 - - + -
545A TYR* 3.8 39.0 - - + +
546A ILE* 4.2 19.1 - - + -
549A LEU* 5.0 2.1 - - + +
584A ILE* 4.2 24.2 - - + -
585A PRO* 4.7 4.5 - - + -
590A LEU* 2.8 40.5 + - + +
591A GLY* 3.5 9.0 - - - +
593A ARG* 1.3 75.5 - - - +
595A ARG* 1.3 58.3 + - - +
597A GLY* 3.0 17.7 + - - -
598A PHE* 3.5 15.3 - - + -
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Residues in contact with ARG 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A ILE* 4.5 13.5 - - + -
586A VAL* 6.1 7.5 - - - +
591A GLY 3.0 19.4 + - - +
592A GLN* 4.0 18.4 + - - +
593A ARG 3.4 0.6 - - - -
594A ILE* 1.3 71.2 - - - +
596A ARG* 1.3 64.6 + - - +
597A GLY 3.0 2.9 + - - -
598A PHE* 3.2 18.5 + - - +
786A GLU* 5.5 1.3 - - - -
827A TRP* 2.9 87.2 + - + +
828A LEU* 3.1 29.2 - - - +
831A LYS* 2.7 41.8 + - - +
832A GLU* 4.2 8.6 + - - -
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Residues in contact with ARG 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A ASP* 3.6 31.1 + - - +
455A TYR* 3.5 38.1 - - + +
592A GLN 3.4 9.3 + - - +
593A ARG* 3.3 13.9 + - - +
594A ILE 3.1 0.6 - - - -
595A ARG* 1.3 78.6 - - - +
597A GLY* 1.3 61.8 + - - +
598A PHE 3.3 0.5 + - - +
599A ILE* 3.7 12.1 - - - +
826A ASP* 3.3 41.8 + - - +
828A LEU* 3.9 14.1 - - + +
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Residues in contact with GLY 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.5 5.8 - - - -
452A ASP* 2.9 31.5 + - - +
455A TYR* 4.0 17.7 - - - -
456A LEU* 4.1 13.9 - - - -
549A LEU* 6.6 0.2 - - - -
593A ARG 3.8 1.8 + - - -
594A ILE 3.0 12.9 + - - -
595A ARG 3.0 1.8 - - - -
596A ARG* 1.3 80.9 - - - +
598A PHE* 1.3 62.3 + - - +
599A ILE 3.3 0.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il